@jbrowse/bandage-core 6.1.1 → 7.0.0
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/chunks/{chunk-GOY6REMT.js → chunk-2LQ5BWT7.js} +1 -1
- package/dist/chunks/{chunk-N62KBLFC.js → chunk-3ZZSX5HN.js} +1 -1
- package/dist/chunks/{chunk-R6ZUK4Y3.js → chunk-4FQTTG5F.js} +1 -1
- package/dist/chunks/{chunk-7UIMNBJT.js → chunk-6UFS3EWI.js} +6 -5
- package/dist/chunks/{chunk-OSDI57GY.js → chunk-7PWMTUAK.js} +27 -24
- package/dist/chunks/{chunk-XJWN753L.js → chunk-AWCMVPVP.js} +1 -1
- package/dist/chunks/{chunk-ZZA2AFB4.js → chunk-CNQSHEBS.js} +1 -1
- package/dist/chunks/{chunk-CS3E4ETM.js → chunk-DRA7733Q.js} +1 -1
- package/dist/chunks/{chunk-X5L37W4J.js → chunk-E7FWQQHP.js} +1 -1
- package/dist/chunks/{chunk-XH43CLO2.js → chunk-EOSVRILX.js} +1 -1
- package/dist/chunks/{chunk-SMQ545MU.js → chunk-EXSXBIMH.js} +1 -1
- package/dist/chunks/{chunk-YMSSF2RK.js → chunk-FP4H7SFT.js} +1 -1
- package/dist/chunks/{chunk-DKOB2OPC.js → chunk-GJMC3PGM.js} +3 -3
- package/dist/chunks/{chunk-PJESIRDU.js → chunk-JFNPL4UT.js} +2 -2
- package/dist/chunks/chunk-L53SXJZI.js +22 -0
- package/dist/chunks/{chunk-ZKGM7VLA.js → chunk-MH5IA57M.js} +1 -1
- package/dist/chunks/{chunk-MREQ7GIA.js → chunk-MLSWIMZO.js} +1 -1
- package/dist/chunks/{chunk-V5BPIOLS.js → chunk-MZ7QQRUJ.js} +1 -1
- package/dist/chunks/{chunk-4EMPBO7S.js → chunk-N6FECAXP.js} +51 -1
- package/dist/chunks/chunk-O4TGF4WS.js +503 -0
- package/dist/chunks/{chunk-CTSBC2O6.js → chunk-OWFPAIJI.js} +1 -1
- package/dist/chunks/{chunk-X4VVPLI5.js → chunk-TQ7VCGJR.js} +1 -1
- package/dist/chunks/{chunk-ZHCDYSA5.js → chunk-VECR253P.js} +1 -1
- package/dist/chunks/{chunk-RX5CSWJW.js → chunk-VST5SR4C.js} +6 -6
- package/dist/chunks/{chunk-T43W7NKK.js → chunk-WEMKWLDF.js} +1 -1
- package/dist/chunks/{chunk-Y3IOTZJA.js → chunk-WFB5TXRA.js} +1 -1
- package/dist/chunks/{chunk-STNG3Y5X.js → chunk-YZ5CCEDH.js} +0 -30
- package/dist/cli/figure.js +33 -36
- package/dist/deletionEdges.js +5 -1
- package/dist/figure.js +22 -22
- package/dist/graphLabels.js +2 -2
- package/dist/index.js +59 -47
- package/dist/labelLayout.js +6 -6
- package/dist/layout/deletionRoutes.js +1 -3
- package/dist/layout/stressEngine.js +11 -0
- package/dist/layout/tubeMapLayout.js +4 -4
- package/dist/layout/walkRowDraw.js +9 -9
- package/dist/layout/walkStrip.js +10 -10
- package/dist/layoutEngines.js +9 -0
- package/dist/layoutModes.js +7 -7
- package/dist/pathColors.js +3 -3
- package/dist/pipeline.js +4 -4
- package/dist/referenceRampCss.js +8 -8
- package/dist/referenceStrip.js +8 -8
- package/dist/renderer/GeometryBuilder.js +7 -7
- package/dist/tubeMap/axis.js +3 -3
- package/dist/tubeMap/coarsen.js +4 -4
- package/dist/tubeMap/genes.js +4 -4
- package/dist/tubeMap/nodeColors.js +8 -8
- package/dist/types/cli/figure.d.ts +2 -0
- package/dist/types/deletionEdges.d.ts +7 -0
- package/dist/types/index.d.ts +5 -2
- package/dist/types/labelLayout.d.ts +0 -1
- package/dist/types/layout/deletionRoutes.d.ts +0 -1
- package/dist/types/layout/stressEngine.d.ts +19 -0
- package/dist/types/layoutEngines.d.ts +2 -0
- package/dist/types/pipeline.d.ts +2 -0
- package/dist/types/version.d.ts +1 -1
- package/dist/util/SpatialIndex.js +3 -3
- package/dist/util/edgeCurves.js +2 -2
- package/dist/util/hitDetection.js +4 -4
- package/dist/version.js +1 -1
- package/dist/viewport.js +5 -5
- package/dist/walkEncoding.js +8 -8
- package/dist/walkHighlight.js +9 -9
- package/dist/walkKey.js +3 -3
- package/package.json +1 -1
package/dist/layoutModes.js
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LAYOUT_MODE_VALUES,
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layoutModeByValue,
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modeUsesLayoutEngine
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} from "./chunks/chunk-
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import "./chunks/chunk-
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import "./chunks/chunk-ST2IBUAN.js";
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import "./chunks/chunk-
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import "./chunks/chunk-ST2IBUAN.js";
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import "./chunks/chunk-3ZZSX5HN.js";
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import "./chunks/chunk-AB35TJST.js";
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import "./chunks/chunk-TAMCZHLW.js";
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import "./chunks/chunk-
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import "./chunks/chunk-N6FECAXP.js";
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import "./chunks/chunk-2CVHXFK7.js";
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import "./chunks/chunk-CPMHA4W5.js";
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import "./chunks/chunk-BPLIXMH7.js";
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package/dist/pathColors.js
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pathGreyCssColor,
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pathLegend
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} from "./chunks/chunk-
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} from "./chunks/chunk-E7FWQQHP.js";
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import "./chunks/chunk-ST2IBUAN.js";
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import "./chunks/chunk-
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import "./chunks/chunk-3ZZSX5HN.js";
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import "./chunks/chunk-AB35TJST.js";
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import "./chunks/chunk-TAMCZHLW.js";
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import "./chunks/chunk-
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import "./chunks/chunk-N6FECAXP.js";
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import "./chunks/chunk-2CVHXFK7.js";
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import "./chunks/chunk-CPMHA4W5.js";
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import "./chunks/chunk-BPLIXMH7.js";
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package/dist/pipeline.js
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forceLayout,
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} from "./chunks/chunk-
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} from "./chunks/chunk-6UFS3EWI.js";
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import "./chunks/chunk-PUG7LXDF.js";
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import "./chunks/chunk-IGVV37VI.js";
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import "./chunks/chunk-72N5DJHZ.js";
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import "./chunks/chunk-CDLPYR5O.js";
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import "./chunks/chunk-
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import "./chunks/chunk-ST2IBUAN.js";
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import "./chunks/chunk-YZ5CCEDH.js";
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import "./chunks/chunk-ST2IBUAN.js";
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import "./chunks/chunk-TAMCZHLW.js";
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import "./chunks/chunk-UVBGRJQX.js";
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import "./chunks/chunk-6JEWNXCQ.js";
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import "./chunks/chunk-
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import "./chunks/chunk-N6FECAXP.js";
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package/dist/referenceRampCss.js
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import "./chunks/chunk-
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} from "./chunks/chunk-VECR253P.js";
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import "./chunks/chunk-VST5SR4C.js";
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import "./chunks/chunk-UMNCCYBN.js";
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import "./chunks/chunk-
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import "./chunks/chunk-
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import "./chunks/chunk-PBENCR5L.js";
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import "./chunks/chunk-WFB5TXRA.js";
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import "./chunks/chunk-E7FWQQHP.js";
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import "./chunks/chunk-ES2N6V56.js";
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import "./chunks/chunk-
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import "./chunks/chunk-ST2IBUAN.js";
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import "./chunks/chunk-3ZZSX5HN.js";
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package/dist/referenceStrip.js
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import "../chunks/chunk-4EMPBO7S.js";
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import type { BubbleSpread } from '../bubbleSpreads.js';
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import type { FigureOptions } from '../figure.js';
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import type { GbzSource } from '../gbzCut.js';
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import type { LayoutEngineKind } from '../layout/stressEngine.js';
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import type { LayoutModeValue } from '../layoutModes.js';
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import type { WalkLayer } from '../walkEncoding.js';
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export interface FigureSpec extends Omit<FigureOptions, 'walks' | 'region' | 'genes' | 'spec' | 'walkStrip'> {
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@@ -11,6 +12,7 @@ export interface FigureSpec extends Omit<FigureOptions, 'walks' | 'region' | 'ge
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layout?: LayoutModeValue;
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quality?: number;
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bubbleSpread?: BubbleSpread;
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engine?: LayoutEngineKind;
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spacing?: number;
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componentSeparation?: number;
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walks?: (string | WalkLayer)[];
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@@ -24,3 +24,10 @@ export declare function deletionArcCurves(nodePositions: Record<string, {
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y: number;
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}[]>, deletion: DeletionEdge, axis: AxisScale, route?: NodeSegment[], stranded?: boolean): import("./util/geometry.js").BezierCurve[] | undefined;
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export declare function deletionEdges(graph: Graph): DeletionEdge[];
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export declare function closableDeletions(graph: Graph, deletions: DeletionEdge[]): Set<number>;
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export interface DeletionDrawing {
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shown: DeletionEdge[];
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bypassed: Map<number, string[]>;
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hidden: ReadonlySet<number>;
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}
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export declare function deletionDrawing(graph: Graph, deletions: DeletionEdge[], show?: boolean): DeletionDrawing;
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package/dist/types/index.d.ts
CHANGED
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@@ -8,6 +8,9 @@ export { NODE_WIDTHS, maxNodeWidthPx, meanDepth, nodeInk, nodeWidthPx, } from '.
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export type { NodeWidth } from './nodeWidths.js';
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export { BUBBLE_SPREADS } from './bubbleSpreads.js';
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export type { BubbleSpread } from './bubbleSpreads.js';
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export { LAYOUT_ENGINES, stressLayout } from './layout/stressEngine.js';
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export type { LayoutEngineKind } from './layout/stressEngine.js';
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export { layoutEngine } from './layoutEngines.js';
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export { REFERENCE_RAMP_MAX_HUE, buildGeometry, computeReferenceRamp, } from './renderer/GeometryBuilder.js';
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export { Canvas2DRenderer } from './renderer/Canvas2DRenderer.js';
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export { getDpr } from './renderer/canvas.js';
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@@ -31,8 +34,8 @@ export type { TubeMapGene } from './tubeMap/genes.js';
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34
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export { connectorAt, drawTubeMapConnectors, referenceNodes, tubeMapConnectors, } from './tubeMap/connectors.js';
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|
export type { Connector, ReferenceNode } from './tubeMap/connectors.js';
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|
export type { TubeMapColumn, TubeMapDrawing } from './layout/tubeMapLayout.js';
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|
-
export { deletionEdges } from './deletionEdges.js';
|
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|
-
export type { DeletionEdge } from './deletionEdges.js';
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|
+
export { deletionDrawing, deletionEdges } from './deletionEdges.js';
|
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|
+
export type { DeletionDrawing, DeletionEdge } from './deletionEdges.js';
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39
|
export { facetLifts, walkHighlight, walkLift } from './walkHighlight.js';
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|
export { rangeText, walkKey, walkPosition } from './walkKey.js';
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|
export { figureSvg } from './figure.js';
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@@ -32,7 +32,6 @@ export interface LabelLayoutSource {
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nodePositions?: Record<string, NodeSegment[]>;
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labelsNodeSizes: boolean;
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|
nodeLengths: Map<string, number>;
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|
-
showDeletionEdges: boolean;
|
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|
deletions: DeletionEdge[];
|
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|
deletionRoutes?: DeletionRoutes;
|
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stranded?: boolean;
|
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@@ -22,7 +22,6 @@ export declare function withDeletionRoutes(graph: Graph, deletions: DeletionEdge
|
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|
routes: Map<number, string>;
|
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23
|
ids: Set<string>;
|
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|
};
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|
-
export declare function closableDeletions(graph: Graph, deletions: DeletionEdge[]): Set<number>;
|
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|
export declare function routeNodes(graph: Graph, deletions: DeletionEdge[], routes: Map<number, string>, drawnOf: (bp: number) => number, opts: BandageScaleOpts): GraphNode[];
|
|
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|
export declare function takeRoutes(positions: Record<string, NodeSegment[]>, routes: Map<number, string>): {
|
|
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|
nodePositions: {
|
|
@@ -0,0 +1,19 @@
|
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1
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+
import type { EngineRequest } from '../pipeline.js';
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|
+
import type { LayoutResult } from '../types.js';
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|
+
export declare const LAYOUT_ENGINES: readonly [{
|
|
4
|
+
readonly value: "fmmm";
|
|
5
|
+
readonly label: "Bandage (FMMM)";
|
|
6
|
+
readonly description: "Bandage's force-directed layout: OGDF's fast multipole multilevel method, compiled to wasm.";
|
|
7
|
+
}, {
|
|
8
|
+
readonly value: "stress";
|
|
9
|
+
readonly label: "Stress (experimental)";
|
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10
|
+
readonly description: "Stress layout by stochastic gradient descent in plain JS: distances along the graph become distances on the page, so the reference reads straight and a repeat loop reads as a ring.";
|
|
11
|
+
}];
|
|
12
|
+
export type LayoutEngineKind = (typeof LAYOUT_ENGINES)[number]['value'];
|
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|
+
export declare const LAYOUT_ENGINE_VALUES: ("fmmm" | "stress")[];
|
|
14
|
+
export interface StressOptions {
|
|
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|
+
quality?: number;
|
|
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|
+
seed?: number;
|
|
17
|
+
componentSeparation?: number;
|
|
18
|
+
}
|
|
19
|
+
export declare function stressLayout(request: EngineRequest, opts?: StressOptions): LayoutResult;
|
package/dist/types/pipeline.d.ts
CHANGED
|
@@ -1,6 +1,7 @@
|
|
|
1
1
|
import type { BubbleSpread } from './bubbleSpreads.js';
|
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2
|
import type { LayoutScaling } from './layout/drawnScale.js';
|
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3
|
import type { LayoutNode } from './layout/referenceSeeds.js';
|
|
4
|
+
import type { LayoutEngineKind } from './layout/stressEngine.js';
|
|
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5
|
import type { Graph, LayoutResult, NodeSegment } from './types.js';
|
|
5
6
|
export interface Bounds {
|
|
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7
|
minX: number;
|
|
@@ -30,6 +31,7 @@ export interface EngineSettings {
|
|
|
30
31
|
spacing?: number;
|
|
31
32
|
componentSeparation?: number;
|
|
32
33
|
showDeletionEdges?: boolean;
|
|
34
|
+
engine?: LayoutEngineKind;
|
|
33
35
|
}
|
|
34
36
|
export declare function engineRequest(graph: Graph, scaling: LayoutScaling, settings: EngineSettings): EngineRequest;
|
|
35
37
|
export declare function engineKey(graph: Graph, settings: EngineSettings): string;
|
package/dist/types/version.d.ts
CHANGED
|
@@ -1 +1 @@
|
|
|
1
|
-
export declare const version = "
|
|
1
|
+
export declare const version = "7.0.0";
|
|
@@ -1,9 +1,9 @@
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|
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1
|
import {
|
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|
EdgeSpatialIndex,
|
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SpatialIndex
|
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-
} from "../chunks/chunk-
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-
import "../chunks/chunk-
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import "../chunks/chunk-
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} from "../chunks/chunk-MLSWIMZO.js";
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import "../chunks/chunk-WFB5TXRA.js";
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package/dist/util/edgeCurves.js
CHANGED
|
@@ -1,7 +1,7 @@
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1
1
|
import {
|
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2
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|
baseEdgeCurves
|
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-
} from "../chunks/chunk-
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-
import "../chunks/chunk-
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|
+
} from "../chunks/chunk-WFB5TXRA.js";
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import "../chunks/chunk-N6FECAXP.js";
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import "../chunks/chunk-2CVHXFK7.js";
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import "../chunks/chunk-CPMHA4W5.js";
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import "../chunks/chunk-FYQWPEEY.js";
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|
@@ -4,10 +4,10 @@ import {
|
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|
findHoveredEdge,
|
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5
|
findHoveredNode,
|
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|
nodesUnderBox
|
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-
} from "../chunks/chunk-
|
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|
-
import "../chunks/chunk-
|
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-
import "../chunks/chunk-
|
|
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-
import "../chunks/chunk-
|
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|
+
} from "../chunks/chunk-FP4H7SFT.js";
|
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+
import "../chunks/chunk-MLSWIMZO.js";
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import "../chunks/chunk-WFB5TXRA.js";
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import "../chunks/chunk-N6FECAXP.js";
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import "../chunks/chunk-CPMHA4W5.js";
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|
package/dist/version.js
CHANGED
package/dist/viewport.js
CHANGED
|
@@ -5,20 +5,20 @@ import {
|
|
|
5
5
|
screenToLayout,
|
|
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|
viewportOf,
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|
zoomAbout
|
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} from "./chunks/chunk-
|
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|
-
import "./chunks/chunk-
|
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|
+
} from "./chunks/chunk-AWCMVPVP.js";
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|
+
import "./chunks/chunk-6UFS3EWI.js";
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import "./chunks/chunk-PUG7LXDF.js";
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import "./chunks/chunk-72N5DJHZ.js";
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import "./chunks/chunk-
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import "./chunks/chunk-ST2IBUAN.js";
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import "./chunks/chunk-YZ5CCEDH.js";
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import "./chunks/chunk-ES2N6V56.js";
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import "./chunks/chunk-ST2IBUAN.js";
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import "./chunks/chunk-TAMCZHLW.js";
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import "./chunks/chunk-UVBGRJQX.js";
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import "./chunks/chunk-6JEWNXCQ.js";
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import "./chunks/chunk-
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+
import "./chunks/chunk-N6FECAXP.js";
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import "./chunks/chunk-2CVHXFK7.js";
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import "./chunks/chunk-CPMHA4W5.js";
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|
import "./chunks/chunk-BPLIXMH7.js";
|
package/dist/walkEncoding.js
CHANGED
|
@@ -9,18 +9,18 @@ import {
|
|
|
9
9
|
schemeColor,
|
|
10
10
|
schemeCss,
|
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11
|
schemeRgb
|
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|
-
} from "./chunks/chunk-
|
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|
-
import "./chunks/chunk-
|
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|
+
} from "./chunks/chunk-TQ7VCGJR.js";
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+
import "./chunks/chunk-VST5SR4C.js";
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|
import "./chunks/chunk-UMNCCYBN.js";
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import "./chunks/chunk-
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import "./chunks/chunk-
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import "./chunks/chunk-
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import "./chunks/chunk-PBENCR5L.js";
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import "./chunks/chunk-WFB5TXRA.js";
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import "./chunks/chunk-E7FWQQHP.js";
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import "./chunks/chunk-
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import "./chunks/chunk-ST2IBUAN.js";
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import "./chunks/chunk-3ZZSX5HN.js";
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import "./chunks/chunk-TAMCZHLW.js";
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-
import "./chunks/chunk-
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import "./chunks/chunk-4EMPBO7S.js";
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import "./chunks/chunk-N6FECAXP.js";
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|
package/dist/walkHighlight.js
CHANGED
|
@@ -2,19 +2,19 @@ import {
|
|
|
2
2
|
facetLifts,
|
|
3
3
|
walkHighlight,
|
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4
4
|
walkLift
|
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|
-
} from "./chunks/chunk-
|
|
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|
-
import "./chunks/chunk-
|
|
7
|
-
import "./chunks/chunk-
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5
|
+
} from "./chunks/chunk-MH5IA57M.js";
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import "./chunks/chunk-TQ7VCGJR.js";
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|
+
import "./chunks/chunk-VST5SR4C.js";
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|
import "./chunks/chunk-UMNCCYBN.js";
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-
import "./chunks/chunk-
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import "./chunks/chunk-
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|
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import "./chunks/chunk-
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+
import "./chunks/chunk-PBENCR5L.js";
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import "./chunks/chunk-WFB5TXRA.js";
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import "./chunks/chunk-E7FWQQHP.js";
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import "./chunks/chunk-ES2N6V56.js";
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-
import "./chunks/chunk-
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+
import "./chunks/chunk-ST2IBUAN.js";
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+
import "./chunks/chunk-3ZZSX5HN.js";
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import "./chunks/chunk-AB35TJST.js";
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import "./chunks/chunk-TAMCZHLW.js";
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-
import "./chunks/chunk-
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import "./chunks/chunk-4EMPBO7S.js";
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import "./chunks/chunk-N6FECAXP.js";
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|
package/dist/walkKey.js
CHANGED
|
@@ -2,11 +2,11 @@ import {
|
|
|
2
2
|
rangeText,
|
|
3
3
|
walkKey,
|
|
4
4
|
walkPosition
|
|
5
|
-
} from "./chunks/chunk-
|
|
6
|
-
import "./chunks/chunk-
|
|
5
|
+
} from "./chunks/chunk-2LQ5BWT7.js";
|
|
6
|
+
import "./chunks/chunk-3ZZSX5HN.js";
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|
import "./chunks/chunk-AB35TJST.js";
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|
import "./chunks/chunk-TAMCZHLW.js";
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import "./chunks/chunk-
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+
import "./chunks/chunk-N6FECAXP.js";
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|
import "./chunks/chunk-CPMHA4W5.js";
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|
import "./chunks/chunk-FYQWPEEY.js";
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@jbrowse/bandage-core",
|
|
3
|
-
"version": "
|
|
3
|
+
"version": "7.0.0",
|
|
4
4
|
"description": "Pangenome graph layout and drawing with no host: GFA in, the Bandage force-directed engine and reference-anchored layouts, a Canvas2D renderer, hit testing and labels out",
|
|
5
5
|
"license": "GPL-3.0-or-later",
|
|
6
6
|
"repository": {
|